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Coexpression cluster:C371: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0494939,0.00208474,0.0469303,0.109533,1.31485,0.71419,0.150903,0.269341,0.127607,4.56192e-05,0.093623,0.525567,0.513421,0.87052,0.134793,0.360925,0.302324,2.86164,0.566995,0.00369674,2.04962,9.03638e-05,0.104721,0.566496,0.228519,0.192028,0.0189,0.103626,0.324953,0.00226539,0.0833716,0.330539,0.0660625,0.522994,0.105498,0.000450463,0.0239955,0.109281,2.7962,0.00691104,0.479124,0.0760943,0.389718,2.25826,0.0362249,0.0580601,0.15155,0.088465,0.487586,0.0347327,0.201351,0.931328,0.131669,0.391649,0.52046,0.14586,1.35462,0.127237,0.11367,0.126682,0.362777,0.152958,0.0459922,0.28158,0.163803,0.256459,2.48253,0.940287,1.55429,0.786982,0.0704501,0.138154,0.0609397,1.28935,1.0083,0.00335784,0.0527547,0.269153,0.319998,9.24362,1.90848,0.280786,4.53773,0.134389,0.474452,5.50467e-06,0.000450536,0.106662,0.218841,1.03562,0.682835,0.451575,0.343662,0.0152379,0.0340178,0.204492,1.46167,0.37755,1.18387,0.00141526,0.216047,0.89974,0.373064,0.305101,0.693347,0.0914534,0.293159,0.142148,0.0638422,0.0294273,0.0508492,0.370843,0.171939,0.0982118,0.63916,4.23032,1.29686e-05,0.0828247,0.254779,0.0157509,2.19909,1.16538,0.348113,0.170544,0.740513,0.269709,0.450707,0.34759,0.548727,0.655014,1.14682,1.00949,0.561391,0.168477,2.79089,0.011561,0.0806627,2.95634,0.655888,1.48038,1.08626,0.62213,2.75106,0.374712,0.249475,0.776936,0.237695,1.32355,0.0746484,0.0146617,0.000624942,0.000113697,0.452479,0.00800229,0.152669,0.815647,0.598763,0.0299572,0.063967,0.0529349,0.621036,1.9502,0.319392,0.0541122,0.261021,0.163104,0.162163,0.895782,0.000396603
|tfbs_overrepresentation_jaspar=MA0003.1;5.76009e-11,MA0004.1;0.0961566,MA0006.1;0.0332857,MA0007.1;0.0871398,MA0009.1;0.417521,MA0014.1;3.07222e-05,MA0017.1;0.0455998,MA0019.1;0.533378,MA0024.1;0.332558,MA0025.1;0.531977,MA0027.1;1.95983,MA0028.1;0.0380705,MA0029.1;0.347825,MA0030.1;0.338746,MA0031.1;6.01545,MA0038.1;0.464214,MA0040.1;0.352485,MA0041.1;0.699566,MA0042.1;0.624693,MA0043.1;0.417784,MA0046.1;0.408463,MA0048.1;0.000993709,MA0050.1;0.301942,MA0051.1;0.150026,MA0052.1;0.355576,MA0055.1;0.0505383,MA0056.1;0,MA0057.1;0.0232745,MA0058.1;0.0546193,MA0059.1;0.199599,MA0060.1;0.0090143,MA0061.1;0.00593062,MA0063.1;0,MA0066.1;0.464855,MA0067.1;0.697961,MA0068.1;0.00295312,MA0069.1;1.84262,MA0070.1;0.396023,MA0071.1;0.12997,MA0072.1;0.392323,MA0073.1;5.91004e-08,MA0074.1;0.149576,MA0076.1;0.060743,MA0077.1;0.386,MA0078.1;0.612611,MA0081.1;2.7739,MA0083.1;0.423797,MA0084.1;0.873335,MA0087.1;0.390315,MA0088.1;0.00127398,MA0089.1;0,MA0090.1;0.066597,MA0091.1;0.0974512,MA0092.1;0.0795385,MA0093.1;0.0341631,MA0095.1;0,MA0098.1;0,MA0100.1;0.485182,MA0101.1;0.0351297,MA0103.1;0.125753,MA0105.1;0.000586518,MA0106.1;0.178189,MA0107.1;0.199846,MA0108.2;0.286605,MA0109.1;0,MA0111.1;1.37617,MA0113.1;0.188804,MA0114.1;0.0161389,MA0115.1;0.62811,MA0116.1;0.0177927,MA0117.1;0.449155,MA0119.1;0.0483167,MA0122.1;1.18789,MA0124.1;0.590699,MA0125.1;0.516292,MA0130.1;0,MA0131.1;0.226279,MA0132.1;0,MA0133.1;0,MA0135.1;0.443024,MA0136.1;0.156833,MA0139.1;0.00480396,MA0140.1;0.403323,MA0141.1;0.05349,MA0142.1;0.265252,MA0143.1;0.188919,MA0144.1;0.0135989,MA0145.1;0.000217103,MA0146.1;1.76994e-06,MA0147.1;0.0184972,MA0148.1;0.1088,MA0149.1;0.123091,MA0062.2;0.00542453,MA0035.2;0.128078,MA0039.2;4.25281e-08,MA0138.2;0.214585,MA0002.2;0.238419,MA0137.2;0.0400993,MA0104.2;0.00891586,MA0047.2;0.170483,MA0112.2;0.000170144,MA0065.2;0.000239994,MA0150.1;0.0641761,MA0151.1;0,MA0152.1;0.132183,MA0153.1;0.501603,MA0154.1;0.00419164,MA0155.1;0.0434015,MA0156.1;0.0408263,MA0157.1;1.97042,MA0158.1;0,MA0159.1;0.018627,MA0160.1;0.116872,MA0161.1;0,MA0162.1;1.86429e-06,MA0163.1;3.47439e-07,MA0164.1;0.196993,MA0080.2;0.0341882,MA0018.2;0.179075,MA0099.2;0.132386,MA0079.2;0,MA0102.2;0.908736,MA0258.1;0.0120495,MA0259.1;0.0202561,MA0442.1;0
}}
}}

Revision as of 19:06, 22 January 2013


Full id: C371_occipital_medial_brain_parietal_amygdala_frontal_olfactory



Phase1 CAGE Peaks

Hg19::chr4:88411966..88411977,-p@chr4:88411966..88411977
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Hg19::chr4:88414835..88414843,-p@chr4:88414835..88414843
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Hg19::chr4:88415052..88415063,-p@chr4:88415052..88415063
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Hg19::chr4:88415241..88415254,-p@chr4:88415241..88415254
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Hg19::chr4:88415266..88415276,-p@chr4:88415266..88415276
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Hg19::chr4:88415315..88415329,-p@chr4:88415315..88415329
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Hg19::chr4:88415383..88415404,-p@chr4:88415383..88415404
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Hg19::chr4:88415409..88415444,-p@chr4:88415409..88415444
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Hg19::chr4:88415461..88415473,-p@chr4:88415461..88415473
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Hg19::chr4:88415581..88415589,-p@chr4:88415581..88415589
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Hg19::chr4:88415590..88415607,-p@chr4:88415590..88415607
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Hg19::chr4:88415610..88415627,-p@chr4:88415610..88415627
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Hg19::chr4:88415629..88415646,-p@chr4:88415629..88415646
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Hg19::chr4:88415711..88415725,-p@chr4:88415711..88415725
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Hg19::chr4:88415731..88415754,-p@chr4:88415731..88415754
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Hg19::chr4:88416158..88416167,-p@chr4:88416158..88416167
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Hg19::chr4:88416205..88416281,-p@chr4:88416205..88416281
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Hg19::chr4:88450273..88450287,-p5@SPARCL1
Hg19::chr4:88450351..88450368,-p2@SPARCL1
Hg19::chr4:88450372..88450424,-p3@SPARCL1
Hg19::chr4:88450428..88450439,-p9@SPARCL1
Hg19::chr4:88450448..88450459,-p7@SPARCL1
Hg19::chr4:88450511..88450533,-p1@SPARCL1
Hg19::chr4:88450535..88450561,-p4@SPARCL1
Hg19::chr4:88450595..88450608,-p6@SPARCL1
Hg19::chr4:88450612..88450623,-p8@SPARCL1
Hg19::chr4:88451026..88451042,-p15@SPARCL1
Hg19::chr7:87338767..87338774,+p2@RUNDC3B
Hg19::chr7:87342602..87342617,-p2@ABCB1
Hg19::chr7:87342681..87342695,-p3@ABCB1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0008559xenobiotic-transporting ATPase activity0.0035321647640094
GO:0042910xenobiotic transporter activity0.0035321647640094
GO:0015239multidrug transporter activity0.0035321647640094
GO:0015238drug transporter activity0.0145663193763842
GO:0042493response to drug0.0333499698628189



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.67e-118114
neural tube5.11e-6356
neural rod5.11e-6356
future spinal cord5.11e-6356
neural keel5.11e-6356
regional part of nervous system5.78e-5853
regional part of brain5.78e-5853
regional part of forebrain1.23e-4841
forebrain1.23e-4841
anterior neural tube1.23e-4841
future forebrain1.23e-4841
neural plate3.52e-4882
presumptive neural plate3.52e-4882
central nervous system6.92e-4681
brain1.61e-4568
future brain1.61e-4568
neurectoderm3.84e-4586
nervous system1.61e-4189
brain grey matter1.54e-3934
gray matter1.54e-3934
telencephalon8.97e-3934
structure with developmental contribution from neural crest5.83e-38132
regional part of telencephalon2.46e-3632
cerebral hemisphere4.04e-3632
ecto-epithelium6.07e-36104
pre-chordal neural plate1.98e-3261
regional part of cerebral cortex5.59e-3022
neocortex1.15e-2620
organ system subdivision9.43e-26223
cerebral cortex1.05e-2525
pallium1.05e-2525
ectoderm-derived structure3.37e-23171
ectoderm3.37e-23171
presumptive ectoderm3.37e-23171
anatomical conduit8.57e-21240
anatomical cluster1.56e-20373
tube2.33e-19192
multi-tissue structure4.26e-17342
basal ganglion8.77e-169
nuclear complex of neuraxis8.77e-169
aggregate regional part of brain8.77e-169
collection of basal ganglia8.77e-169
cerebral subcortex8.77e-169
neural nucleus1.14e-159
nucleus of brain1.14e-159
posterior neural tube5.60e-1515
chordal neural plate5.60e-1515
organ5.98e-14503
organ part2.15e-13218
telencephalic nucleus1.82e-127
segmental subdivision of nervous system9.43e-1213
diencephalon3.36e-117
future diencephalon3.36e-117
gyrus5.49e-116
epithelium9.47e-11306
segmental subdivision of hindbrain1.79e-1012
hindbrain1.79e-1012
presumptive hindbrain1.79e-1012
cell layer1.82e-10309
brainstem2.14e-106
multi-cellular organism3.01e-10656
limbic system1.15e-095
anatomical system2.22e-09624
anatomical group2.56e-09625
temporal lobe3.98e-096
embryonic structure6.75e-09564
parietal lobe1.26e-085
embryo1.30e-08592
germ layer1.36e-08560
germ layer / neural crest1.36e-08560
embryonic tissue1.36e-08560
presumptive structure1.36e-08560
germ layer / neural crest derived structure1.36e-08560
epiblast (generic)1.36e-08560
developing anatomical structure2.66e-08581
corpus striatum5.35e-084
striatum5.35e-084
ventral part of telencephalon5.35e-084
future corpus striatum5.35e-084
regional part of diencephalon3.15e-074
gland of diencephalon9.17e-074
neuroendocrine gland9.17e-074


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.15.76009e-11
MA0004.10.0961566
MA0006.10.0332857
MA0007.10.0871398
MA0009.10.417521
MA0014.13.07222e-05
MA0017.10.0455998
MA0019.10.533378
MA0024.10.332558
MA0025.10.531977
MA0027.11.95983
MA0028.10.0380705
MA0029.10.347825
MA0030.10.338746
MA0031.16.01545
MA0038.10.464214
MA0040.10.352485
MA0041.10.699566
MA0042.10.624693
MA0043.10.417784
MA0046.10.408463
MA0048.10.000993709
MA0050.10.301942
MA0051.10.150026
MA0052.10.355576
MA0055.10.0505383
MA0056.10
MA0057.10.0232745
MA0058.10.0546193
MA0059.10.199599
MA0060.10.0090143
MA0061.10.00593062
MA0063.10
MA0066.10.464855
MA0067.10.697961
MA0068.10.00295312
MA0069.11.84262
MA0070.10.396023
MA0071.10.12997
MA0072.10.392323
MA0073.15.91004e-08
MA0074.10.149576
MA0076.10.060743
MA0077.10.386
MA0078.10.612611
MA0081.12.7739
MA0083.10.423797
MA0084.10.873335
MA0087.10.390315
MA0088.10.00127398
MA0089.10
MA0090.10.066597
MA0091.10.0974512
MA0092.10.0795385
MA0093.10.0341631
MA0095.10
MA0098.10
MA0100.10.485182
MA0101.10.0351297
MA0103.10.125753
MA0105.10.000586518
MA0106.10.178189
MA0107.10.199846
MA0108.20.286605
MA0109.10
MA0111.11.37617
MA0113.10.188804
MA0114.10.0161389
MA0115.10.62811
MA0116.10.0177927
MA0117.10.449155
MA0119.10.0483167
MA0122.11.18789
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.226279
MA0132.10
MA0133.10
MA0135.10.443024
MA0136.10.156833
MA0139.10.00480396
MA0140.10.403323
MA0141.10.05349
MA0142.10.265252
MA0143.10.188919
MA0144.10.0135989
MA0145.10.000217103
MA0146.11.76994e-06
MA0147.10.0184972
MA0148.10.1088
MA0149.10.123091
MA0062.20.00542453
MA0035.20.128078
MA0039.24.25281e-08
MA0138.20.214585
MA0002.20.238419
MA0137.20.0400993
MA0104.20.00891586
MA0047.20.170483
MA0112.20.000170144
MA0065.20.000239994
MA0150.10.0641761
MA0151.10
MA0152.10.132183
MA0153.10.501603
MA0154.10.00419164
MA0155.10.0434015
MA0156.10.0408263
MA0157.11.97042
MA0158.10
MA0159.10.018627
MA0160.10.116872
MA0161.10
MA0162.11.86429e-06
MA0163.13.47439e-07
MA0164.10.196993
MA0080.20.0341882
MA0018.20.179075
MA0099.20.132386
MA0079.20
MA0102.20.908736
MA0258.10.0120495
MA0259.10.0202561
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C371&oldid=2568882"